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Analysis of the baseline survey on the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in holdings with breeding pigs, in the EU, 2008 [1] - Part A: MRSA prevalence estimates

EFSA Journal 2009; 7(11):1376[82 pp.]. doi:10.2903/j.efsa.2009.1376
European Food Safety Authority Acknowledgment EFSA wishes to thank the members of the Task Force on Zoonoses Data Collection that endorsed this report: Andrea Ammon, Alenka Babusek, Lisa Barco, Marta Bedriova, Susan Chircop, Marianne Chriel, Georgi Chobanov, Ingrid Dan, Jürg Danuser, Noel Demicoli, Kris De Smet, Sylvie Francart, Matthias Hartung, Birgitte Helwigh, Merete Hofshagen, Patrícia Inácio, Sarolta Idei, Elina Lahti, Lesley Larkin, Peter Much, Edith Nagy, Lisa O’Connor, Rob Van Oosterom, Jacek Osek, José Luis Paramio Lucas, Antonio Petrini, Melanie Picherot, Christodoulos Pipis, Saara Raulo, Petr Šatrán, Joseph Schon, Jelena Sõgel, Snieguole Sceponaviciene, Ana María Troncoso González, Kilian Unger, Luc Vanholme, Dimitris Vourvidis, Nicole Werner-Keišs. The contribution of the members of the working group that prepared this scientific report is gratefully acknowledged: Hanne-Dorthe Emborg, Concepción Porrero, Pascal Sanders, Gertraud Schuepbach, Christopher Teale, Bernd-Alois Tenhagen, and Jaap Wagenaar; and that of EFSA’s contractors: Hendriek Boshuizen from National Institute for Public Health and Environment (RIVM); Frank Aarestrup and Henrik Hasman from Danish Technical University, National Food Institute, as well as EFSA’s staff members: Pierre-Alexandre Belœil, Giusi Amore, Francesca Riolo, and Frank Boelaert for the support provided to this EFSA scientific output. Contact zoonoses@efsa.europa.eu
Type: Scientific Report of EFSA On request from: European Commission Question number: EFSA-Q-2008-417A Published: 24 November 2009 Affiliation: European Food Safety Authority (EFSA), Parma, Italy
Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) has been recognised as an important cause of hospital-associated infections in humans for several decades. MRSA is resistant to the most commonly used antibiotics. The MRSA lineage ST398 (MRSA ST398) has been recently described as a cause of infection for people occupationally exposed to pigs, by direct or indirect contact. MRSA ST398 can occasionally be introduced into hospitals as a result of community-acquired human infections. To assess the occurrence and the diversity of MRSA in pig primary production, a European Union-wide preliminary survey was carried out in parallel with a baseline survey on Salmonella spp. in holdings with breeding pigs to determine the prevalence of holdings positive for MRSA and MRSA ST398.

© European Food Safety Authority,2009

Summary

Methicillin-resistant Staphylococcus aureus (MRSA) has been recognised as an important cause of hospital-associated infections in humans for several decades. MRSA is resistant to the most commonly used antibiotics. The MRSA lineage ST398 (MRSA ST398) has been recently described as a cause of infection for people occupationally exposed to pigs, by direct or indirect contact. MRSA ST398 can occasionally be introduced into hospitals as a result of community-acquired human infections. To assess the occurrence and the diversity of MRSA in pig primary production, a European Union-wide preliminary survey was carried out in parallel with a baseline survey on Salmonella spp. in holdings with breeding pigs to determine the prevalence of holdings positive for MRSA and MRSA ST398.

Sampling took place between January 2008 and December 2008. Five dust samples were taken in the immediate environment of breeding pigs in the holdings. The pooled sample of each holding was tested for the presence of MRSA and all isolates were sub-typed by spa-typing and where necessary by Multi-Locus Sequence Typing (MLST). On the basis of typing results, isolates were classified as either belonging to MRSA ST398 or to other sequence types. A total of 1,421 holdings housing and selling mainly breeding pigs (breeding holdings), and 3,176 holdings housing breeding pigs and selling mainly pigs for fattening or slaughter (production holdings) from 24 European Union Member States were included in the survey. Also, two countries not belonging to the European Union (non-Member States) participated in the survey. Seventeen Member States detected MRSA in their breeding or production holdings whereas seven Member States did not detect any MRSA in the surveyed holdings. MRSA was more often detected in production holdings than in breeding holdings. The European Union prevalence of MRSA positive holdings with breeding pigs, as estimated based on the results from the 24 participating Member States, was 22.8%. MRSA ST398 was the predominant MRSA lineage identified in the holdings with breeding pigs in the European Union, counting for 92.5% of the MRSA isolates.

The results were analysed separately for breeding holdings and production holdings, due to the expected differences in MRSA occurrence in those types of holdings. Twelve of the 24 Member States isolated MRSA in breeding holdings, which resulted in a European Union prevalence of breeding holdings positive for MRSA and for MRSA ST398 of 14.0% and 13.1%, respectively. Prevalence varied widely among the Member States, from 0% to 46.0%. One Member State reported MRSA isolates not belonging to lineage ST398 (MRSA non-ST398). Neither of the two non-Member States found MRSA in their breeding holdings.

Sixteen Member States and one non-Member State detected MRSA in production holdings, while eight Member States did not. The European Union prevalence of MRSA and of MRSA ST398 positive production holdings was 26.9% and 25.5%, respectively. The prevalence of MRSA and of MRSA ST398 positive production holdings also varied widely among MSs, from 0% to 51.2% and from 0% to 50.2%, respectively. Only six Member States and one non-Member State reported isolates of MRSA non-ST398, resulting in a low European Union prevalence of non-ST398 positive production holdings of 1.4% (range from 0% to 12.3%).

The prevalence presented in the report are observed prevalence, meaning that the prevalence estimates do not account for potential imperfect test characteristics. The MRSA prevalence estimates from this preliminary survey may underestimate the true prevalence due to a possible lack of sensitivity of the pooled environmental samples taken.

In this survey, the most frequently isolated spa-types belonging to MRSA ST398 were t011, t108 and t034. In addition, spa-types belonging to MRSA non-ST398 were detected in production holdings and, to a lesser extent, in breeding holdings. In particular, spa-types belonging to lineages ST5, ST8, and ST132, which are spa-types known in human medicine, were each isolated in different production holdings. Colonisation of pigs with MRSA ST398 has been identified as an occupational health risk for farmers, veterinarians and their families. Such information is not available for the MRSA non-ST398 strains isolated in this survey from pig holdings and which have also been detected in humans.

It is recommended that the information from this preliminary survey be complemented by monitoring of MRSA in breeding and fattening pigs as well as in other food-producing animal species such as poultry and cattle. Also investigations of the causes of variation in MRSA prevalence among the Member States as well as of the human health importance of the MRSA non-ST398 findings in pigs and the role of humans as potential sources of these strains are recommended.

Keywords

MRSA, spa-typing, MLST, pigs, breeding pigs, prevalence, EU.